Welcome to vesiweb

With vesiweb you can control vesimulus, the tool for stochastic molecular
simulation of chromatophore vesicles from Rhodobacter
sphaeroides. This web frontend allows you to edit the parameters
for the simulation, i.e., the numbers of the corresponding proteins, the
reaction rates and the initial number of metabolite particles. After
the simulation is finished, you can analyze the outcome of your
simulations.

If you visit vesiweb for the first time, you might want to take a look
at the
tutorials, which should give you an impression of what
you can do with vesiweb and how to use it.
For some more help on the model and the parameters, check the online Help page and look out for "(?)"-signs for help.

Motivation

Systems biology is trying to understand cells - or at least parts
thereof - in its entirety. Its aim is to build up a model of all
processes on all levels of the organism (genome, proteome, metabolome,
...), to be able to understand and explain its function and its
behavior.
In the future, computer based simulations will be able to simulate
whole cells, but today one tries to find methods and algorithms to
reliably describe such biological systems. As a tool to learn how to
build molecular models, handle their complexity and to finally figure
out their inner working, we here present a molecular model of the small
chromatophore vesicles from the purple bacterium Rhodobacter
sphaeroides. These small 50 nm sized vesicles are covered with the
proteins of the bacteria's photosynthetic apparatus. The system to be
simulated only contains some 100 proteins of 4 different types and two
types of transporter molecules. Due to its simplicity and due to the
fact that they can be probed very easily with light signal, they are a
perfect system for cell biology and basic research on molecular
systemic simulations.